ChemDoodles, ISISDraw, BKChem, MarvinBeans, ChemSketch, ChemDraw…

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There’s at least a dozen chemical structure editors running under different kinds of licenses and platform, and (ugh) none of them are truly satisfactory.  The latest one I’ve checked out is ChemDoodle, which is somewhat new and have some good things going on.  The existing reviews on the Net dates to 2004/5, so a fresh look at the current capabilities will be useful to the chemist community.  A more comprehensive look will come later (as in, a month or two later); this post is interim notes to remind myself for later, and an invitation for readers’ comments.  What other sketching software should I know about and what are your experiences with them?

ChemDraw (CambridgeSoft): the “industrial standard” (that I detest).  Locks files in proprietary CDX formats, pricey even for academic versions, never updated.  You pay for each platform and features are deliberately crippled on the “lower end” versions (really?  I need to pay through the nose to get SMILES import?)  Rotware.  Closed sourced (obviously; C++ code?), good bunch of templates and assets, mature interfacing with other stuff in its suite (Notebook etc.)  I’ve always thought of them as the real-world equivalent of a kinetic trap.  Not extensible (at least in my version).

ISISDraw (Accelrys): Back in the day, the only free equivalent to ChemDraw.  Windows only. Abandonware; wikipedia reports that it is superceded by Symyx Draw.  Haven’t tried it out since.  Uses .skc as main operation file-format.

ChemSketch (ACDLabs): free structure drawing program for Windows (Wine emulation on OSX/ linux doesn’t count!)  Need to look more into it – last time I checked there was relatively limited templates.

BKChem (Beda Kosata, and is currently maintained by Reinis Danne): I love open-source software and I love python (platform-independent), so technically this is great.  A quick test found it a little klutzy, the way python software are often klutzy.  I haven’t tried the latest version since it’s maintained by Reinis Danne, so it’ll be on the to-do list.

MarvinBeans (ChemAxon): Java; cross-platform, comes with 3D/space visualization tools.  Uses a wide variety of format.  Very cheminformatics driven and feature-rich in that regard (Markush enumerations etc).  Free for academic use (citation-ware).  My impression is that this is the best for now.

ChemDoodles (iChemLab): a new-comer, has a uniform pricing of $60, and one that get me excited enough that I feel it’ll be a good competitor to MarvinBeans.  It has a web-driven focus, with ability to export stuff (anim/struct.) as web-components to HTML5 browsers.  It has limited assets ATM (e.g., templates), but the super-cool ability to sub-structure search on local computer and do pubchem pulls (Either MarvinBean or Ball-project claim the same PubChem pull feature but on my version it never pull the right molecule.).  The latter seems to have limitations about stereochemistry (it may be a deficiency of pubchem, or SMILES representation?), but it works, as well as spectra prediction, and funky stuff not found elsewhere like pseudo-3D rotations (as a supramolecular chemist I think this is a god-send).  The UI of Doodle can be improved – not hard to figure out, but my sense is that in future versions it will be more polished.  Great variety of input/output options.

Doodles open-sources the JavaScript web-components – it’s a little mystifying to me – couldn’t someone just use that to make a web-app that does exactly what the retail version does?  Since I’ve been playing with Google Web Toolkit, Java, and JS lately, I’ll actually give this a try when the thesis is done – for my wikipedia work I want a simple app that does simple but rigorous MD calculations (and I think the world can use that too). The ChemDoodle interface is definitely much sleeker than the some other JS-based alternatives (e.g. PubChem).  I am in general curious to crack open the JS package – browsing through the docs, they talk about classes, but I thought JS is real low level and don’t do classes…

Misc.: Screen through other editors.

Table entries useful for the review: name, company, pricing (ind.), pricing (acad.), trial, platform, extensibility, source code, open source?, unique features, attached gadget suites, assets, last updated, misc comments, automatic coloring of atoms?, file formats

Edit 1: If the review is to be comprehensive, it would be useful to segregate by applications.

Edit 2: In case any reader wonders — I have no contact with any of these companies or individuals, no dogs in the fight.


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